You could set the CPU % a bit higher and monitor the CPU and motherboard temperatures from time to time. If they are overheating it isn't the fault of running a workunit at 100%; something needs to be cleaned or fixed.
I have to agree here. I live in central Florida, so I can't leave all my PC's crunching all the time due to heat. However, my Mac PPC G5 has been running since I got it. It goes off when I'm on vacation, but otherwise one core runs BOINC and the other F@H 24/7, rebooting for system updates. My Linux box stays on late fall through early spring, and my windows box stays on early fall through late spring. So far, the only thing that has broke is (also) the south bridge fan on my nVidia motherboard. Since I read that happens every couple years, I bought a large heat sync.
I always recommend that if you build your own PC, always get a heat sync rated for at least one processor model up, or for low overclocking. (I upgraded my heat syncs for BOINC.) That way you're more sure that it will keep a processor pegged at 100% cool. Also, get good thermal compound and be generous in its application. Additionally, an extra cooling fan on the case, preferably blowing across the CPU fan, is a good idea. The extra case fan can be a low speed / quiet model.
If heat or power consumption are the issue, then, yes, cut the processor usage.